MOLECULAR-MODELS AND STRUCTURAL COMPARISONS OF NATIVE AND MUTANT CLASS-I FILAMENTOUS BACTERIOPHAGES FF (FD, F1, M13), IF1 AND IKE
MOLECULAR-MODELS AND STRUCTURAL COMPARISONS OF NATIVE AND MUTANT CLASS-I FILAMENTOUS BACTERIOPHAGES FF (FD, F1, M13), IF1 AND IKE
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DOI：
10.1016/s0022-2836(05)80032-4
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发表时间：
1994-01-07
影响因子：
5.6
通讯作者：
CITTERICH, MH
中科院分区：
文献类型：
--
作者：
MARVIN, DA;HALE, RD;CITTERICH, MH
丝状噬菌体是长约1至2μm、直径约6 nm的柔性杆状体，具有围绕DNA核心的蛋白质亚基螺旋壳。大约50个残基的外壳蛋白亚基主要是α-螺旋，α-螺旋的轴与病毒粒子的轴成小角度。蛋白质外壳可分为三个部分：外表面，由亚基的N-末端区域占据，富含酸性残基，这些残基与周围的溶剂相互作用，使病毒粒子具有低等电点;外壳的内部，包括一段19个残基的非极性侧链，其中蛋白质亚基主要相互作用;内表面由亚基的C-末端区域占据，富含与DNA核心相互作用的碱性残基。事实上，几乎所有的蛋白质侧链之间的相互作用是在不同的亚基在外壳蛋白阵列，而不是在亚基内，这使得它成为一个有用的模型系统的α-螺旋亚基之间的相互作用的研究在一个大分子assembly.We描述的第一类丝状噬菌体的分子模型。该类包括菌株fd、f1、M13（这3种非常相似的菌株是Ff组的成员）、If 1和IKe。我们的fd模型已被完善，以适应定量X射线纤维衍射数据，以30 <$N分辨率在赤道方向和7 <$N分辨率在赤道方向。由该模型得到的3·3 μ m分辨率的模拟衍射图与实验衍射图具有相同的强度分布。用我们的分子模型计算的衍射图比用密度均匀的棒状物表示的模型更好地拟合了在7 μ m分辨率下观察到的衍射数据，我们的fd模型解释了fd衍射数据只是我们结构分析的一部分。该模型的原子细节支持非衍射数据，部分以前发表的，部分新报告在这里。这些数据包括关于允许或禁止的侧链替换、关于化学修饰的效果以及关于光谱实验的信息。侧链比较包括其他I类野生型菌株，它们具有相似的衍射图和相似的氨基酸残基类型的总体分布，但不同的详细序列;先前报道的Ff菌株的突变体，特别是在酸性N-末端区域和碱性C-末端区域;在蛋白质外壳内部的新突变体，其中一些是可行的（F11 Y、Y21 M、I22 V和Y24 M），以及其它携带明显致死突变（F11 M、A27 P以及Ile 22和Ile 32交换为其它非极性残基）的突变。
The filamentous bacteriophages are flexible rods about 1 to 2μm long and 6 nm in diameter, with a helical shell of protein subunits surrounding a DNA core. The approximately 50-residue coat protein subunit is largelyα-helix and the axis of theα-helix makes a small angle with the axis of the virion. The protein shell can be considered in three sections: the outer surface, occupied by the N-terminal region of the subunit, rich in acidic residues that interact with the surrounding solvent and give the virion a low isoelectric point; the interior of the shell, including a 19-residue stretch of apolar side-chains, where protein subunits interact mainly with each other; and the inner surface, occupied by the C-terminal region of the subunit, rich in basic residues that interact with the DNA core. The fact that virtually all protein side-chain interactions are between different subunits in the coat protein array, rather than within subunits, makes this a useful model system for studies of interactions betweenα-helix subunits in a macromolecular assembly.We describe molecular models of the class I filamentous bacteriophages. This class includes strains fd, f1, M13 (these 3 very similar strains are members of the Ff group), If1 and IKe. Our model of fd has been refined to fit quantitative X-ray fibre diffraction data to 30 Å resolution in the meridional direction and 7 Å resolution in the equatorial direction. A simulated 3·3 Å resolution diffraction pattern from this model has the same general distribution of intensity as the experimental diffraction pattern. The observed diffraction data at 7 Å resolution are fitted much better by the calculated diffraction pattern of our molecular model than by that of a model in which theα-helix subunit is represented by a rod of uniform density.The fact that our fd model explains the fd diffraction data is only part of our structure analysis. The atomic details of the model are supported by non-diffraction data, in part previously published and in part newly reported here. These data include information about permitted or forbidden side-chain replacements, about the effect of chemical modification, and about spectroscopic experiments. The side-chain comparisons include the other class I wild-type strains, which have similar diffraction patterns and similar overall distributions of amino-acid residues by type, but different detailed sequences; previously reported mutants of Ff strains, especially in the acidic N-terminal region and the basic C-terminal region; and new mutants in the interior of the protein shell, some of which are viable (F11Y, Y21M, I22V and Y24M), and others of which carry apparently lethal mutations (F11M, A27P and exchanges of Ile22 and Ile32 for other apolar residues).